ws2.slim

// set up a simple neutral simulation
initialize() {
	initializeMutationRate(1e-7);
	
	// m1 mutation type: 
	initializeMutationType("m1", 0.5, "f", 0.0); //neutral
	initializeMutationType("m2", 0.1, "e", 0.1); // benifical
	initializeMutationType("m3", 0.2, "g", -0.03, 0.2); //deliterious 
	// g1 genomic element type: uses m1 for all mutations
	initializeGenomicElementType("g1", m1, 1.0);
	initializeGenomicElementType("g2", c(m1, m2, m3), c(100, 1, 10));
	initializeGenomicElementType("g3", c(m1, m3), c(90, 10));
	// uniform chromosome of length 100 kb with uniform recombination
	initializeGenomicElement(g1, 0, 19999);
   initializeGenomicElement(g2, 20000, 29999);
   initializeGenomicElement(g1, 30000, 59999);
   initializeGenomicElement(g2, 60000, 69999);
	initializeGenomicElement(g3, 70000, 71999);
	initializeGenomicElement(g2, 72000, 79999);
   initializeGenomicElement(g1, 80000, 99999);
	initializeRecombinationRate(1e-8);
}

// create a population of 500 individuals
1 {
	sim.addSubpop("p1", 500);
}

// output samples of 10 genomes periodically, all fixed mutations at end
1000 late() { p1.outputSample(10); }
2000 late() { p1.outputSample(10); }
20000 late() { sim.outputFixedMutations(); }